Characterization of carrier-mediated transport systems for small neutral amino acids in human fibroblast lysosomes

Analog inhibition studies of the uptake of proline, serine, and threonine into human fibroblast lysosomes, purified on Percoll gradients, reveal the presence of three new transport systems. These systems fail to show the Na+ requirement usual for the plasma membrane. Proline uptake into fibroblast lysosomes occurs mainly by two routes: a predominant route half-saturating at 0.01 mM, and a lower-affinity route, half-saturating at 0.07 mM. The latter so far appears specific for L-proline and its 3,4-dehydro derivative. The high affinity route has a broad scope, recognizing best, beyond these two amino acids, various unbranched neutral amino acids not over 5 carbons long. Neither system accepts to a significant extent D-proline, hydroxyproline, cationic or anionic amino acids, nor neutral ones with bulky side chains. 2-Aminoisobutyrate and its N-methyl derivative have little effect on proline uptake, in contrast to their effectiveness on its uptake by the intact fibroblast. The rate of lysosomal proline uptake maximizes at about pH 6.4, is inversely related to the osmolarity of the medium, and is unaffected by the extralysosomal presence of MgATP. The competition among alanine, serine, and threonine points to sharing of the broad-scope system for proline, although the main part of their uptake occurs by a third route that rejects amino acids in which the alpha-amino group is methylated.     

Accumulation of amino acids by lysosomes incubated with amino acid methyl esters.

Rat liver lysosomal preparations incubated with 10(-5) M L-[4,5-3H]leucine methyl ester hydrolyzed the methyl ester and accumulated radioactivity within a particulate compartment. The acculated radioactivity was identified as free leucine by thin layer chromatography. Free leucine was not itself taken up by the lysosomal preparations. The capacity to accumulate leucine was identified as a specific property of lysosomes and was thought to result from the trapping of the free amino acid within the lysosome following the hydrolysis of the methyl ester. Lysosomes also accumulated phenylalanine, serine, and alanine when incubated with the corresponding methyl esters. Leucine accumulation was inhibited by submillimolar concentrations of chloroquine, by the protease inhibitor L-1-tosylamido-2-phenylethyl chloromethyl ketone, and by lowering the pH below 7.0. Efflux of leucine from the lysosomes was highly temperature dependent (activation energy 33 kcal/mol). No evidence was found to suggest that leucine efflux was a carrier-mediated process. The results provide a new methodology for the study of amino acid movements across lysosomal membranes.     

Mass spectrometry in the study of bioclasters of amino acids and peptides]

The study of homo- and heterocluster quasimolecular ions of 20 L-amino acids (A) and five dipeptides by the TOF-PDMS method indicated that the intensity of quasimolecular ions of the corresponding homo-([An + H]+ and [Bm + H]+, where A and B are biomolecules (A, dipeptides), n and m = 1 .... 5) and heteroclusters ([An.Bm + H]+, n and m = 1 .... 5) depends mainly on the hydrophobicity of the constituents of the A cluster. The most intensive peaks of homo- and heterocluster ions were obtained for hydrophobic amino acids: L-Ile, L-Leu, L-Val, and L-Phe, and for dipeptides containing these amino acids. The assumption is made that the stereochemical parameters of heterocluster quasimolecular ions in the TOF-PDMS method are determined by the physicochemical mechanisms involved in the processes of ionization/desorption of biomolecules and do not reflect directly biologically significant interactions of biomolecules in vivo.     

A simple method to detect contaminating peptides and amino acids in large-scale ganglioside preparations

A reverse-phase liquid chromatography method was developed to analyse the presence of contaminating peptides and amino acids in large-scale monosialoganglioside preparations. Samples were hydrolysed under controlled conditions and derivatized with phenylisothiocyanate. PTC-amino acids were then separated and identified by HPLC. The sensitivity of the method allowed detection of a least 50 pmoles of amino acid per mg of ganglioside with excellent reproducibility and little or no interference of by-products derived from hydrolysis of the glycosphingolipid. The response was consistently linear for each amino acid within the examined analytical range. The ease and speed of performance make this method a useful tool for rapidly monitoring large-scale extraction and purification processes of biologicals obtained from natural sources.     

Hydrodynamically coupled water in surface adsorbed amino acids as a tool to study hydrated peptides

The influence of different amino acid residues on properties of a protein surface is of great interest and importance. Hydrodynamically coupled water in the amino acids has the potential to be used as a tool to study surface properties of proteins. The contribution of this coupled water fraction in design of a hydropathy scale in surface adsorbed amino acid films on solid using quartz crystal microbalance is presented in this work. This scale compares well with the hydropathy scale of Guy reported in the literature and can be correlated with the solid/liquid interfacial tension and work of adhesion of the adsorbed amino acid films. Using Graphical Representation and Analysis of Surface Properties (GRASP) the free energy of transfer from Octanol to water for the amino acids has been estimated and shows approximately an inverse relationship with the coupled water fraction. This scale has been applied in a benchmark test for a native Laminin peptide YIGSR and its mutated sequences (with mutations carried out at 'Y and 'R' positions). The experimentally measured coupled water fractions seem to compare well with that obtained from the present scale assuming the total solvent fraction to be a linear function of the amino acids in the sequence. A survey of the protein data bank showed that sets of sequences based on this scale occur in membrane insertion domain or in trans-membrane proteins suggesting that the scale is suitable to study structure-function correlation in proteins.     

Hypochlorite-induced oxidation of amino acids, peptides and proteins

Summary. Activated phagocytes generate the potent oxidant hypochlorite (HOCl) via the release of the enzyme myeloperoxidase and hydrogen peroxide. HOCl is known to react with a number of biological targets including proteins, DNA, lipids and cholesterol. Proteins are likely to be major targets for reaction with HOCl within a cell due to their abundance and high reactivity with HOCl. This review summarizes information on the rate of reaction of HOCl with proteins, the nature of the intermediates formed, the mechanisms involved in protein oxidation and the products of these reactions. The predicted targets for reaction with HOCl from kinetic modeling studies and the consequences of HOCl-induced protein oxidation are also discussed.     

Computer-assisted assignment of peptides with non-standard amino acids

Summary A comprehensive peptide assignment program and its application to a cyclic peptide, cyclosporin A, are presented in this paper. A group of graph theoretical algorithms using fuzzy logic are discussed with the aid of examples from cyclosporin A. The algorithms deal with heavily overlapped peaks, recover disjointed and distorted spin coupling networks, and include strategies for sequence-specific assignment. A procedure to extend the Protein Knowledge Base for automatically assigning non-standard amino acid residues is also presented. The program is capable of completely automated assignment for small peptides (20 residues). For such molecules, it is insensitive to whether the peptide chain is cyclic or acyclic, and to whether amide protons are present or absent. For larger peptides/proteins, more user interaction is required and the sequence-specific assignment step usually must proceed through fragments smaller than the full length to avoid problems due to occurrence of a combinatorial explosion. The program can be applied as a rigorous tool to check manual assignments. The fuzzy graph theoretical concepts built in the program are illustrated with 2D proton spectra of a peptide, but may be extended to higher-dimensional spectra, other biopolymers, natural products and other organic structures.     

Metal-ligated amino acids and peptides as substrates for proteases

Amino acids and peptides carrying a pentaamminecobalt(III) group at the carboxyl terminal have been prepared. It is shown that trypsin and papain accept such compounds as substrates provided the metal complex group is not too close to the enzyme-susceptible peptide bond. The possible applicability of this novel type of substrates in enzymatic peptide synthesis is discussed.